Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: 9MGM2

Calculation Name: 3AEV-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AEV

Chain ID: B

ChEMBL ID:

UniProt ID: O58655

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1928547.252563
FMO2-HF: Nuclear repulsion 1857033.93061
FMO2-HF: Total energy -71513.321953
FMO2-MP2: Total energy -71727.653967


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:26:ASP)


Summations of interaction energy for fragment #1(B:26:ASP)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-45.881-40.5162.82-3.509-4.6760.017
Interaction energy analysis for fragmet #1(B:26:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.958 / q_NPA : -0.991
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B28TRP0-0.030-0.0242.901-11.852-8.6500.416-1.599-2.0190.012
4B29GLU-1-0.858-0.9302.39231.94733.4532.400-1.750-2.1570.005
5B30GLU-1-0.926-0.9643.89139.38740.0440.004-0.160-0.5000.000
6B31PHE0-0.047-0.0165.979-6.652-6.6520.0000.0000.0000.000
7B32PHE0-0.063-0.0377.430-3.591-3.5910.0000.0000.0000.000
8B33LYS10.7170.8776.791-38.368-38.3680.0000.0000.0000.000
9B34GLN0-0.011-0.0038.835-2.544-2.5440.0000.0000.0000.000
10B35GLU-1-0.878-0.95810.35028.35628.3560.0000.0000.0000.000
11B36GLU-1-0.804-0.89213.46314.15314.1530.0000.0000.0000.000
12B37TYR0-0.075-0.05916.7690.2950.2950.0000.0000.0000.000
13B38VAL0-0.0080.00018.885-0.782-0.7820.0000.0000.0000.000
14B39LYS10.8500.91222.353-11.997-11.9970.0000.0000.0000.000
15B40ILE0-0.061-0.01825.154-0.487-0.4870.0000.0000.0000.000
16B41PRO0-0.045-0.02327.9630.0090.0090.0000.0000.0000.000
17B42LYN00.1600.06130.1090.0410.0410.0000.0000.0000.000
18B43ASP-1-0.869-0.90631.3569.1179.1170.0000.0000.0000.000
19B44ARG10.7760.89030.427-9.407-9.4070.0000.0000.0000.000
20B45ILE00.0610.05626.3530.1970.1970.0000.0000.0000.000
21B46ALA00.0110.00127.9600.2210.2210.0000.0000.0000.000
22B47VAL0-0.068-0.02730.168-0.030-0.0300.0000.0000.0000.000
23B48LEU00.0420.02023.587-0.031-0.0310.0000.0000.0000.000
24B49ILE00.0380.03124.3070.3540.3540.0000.0000.0000.000
25B50GLY00.0450.02426.0740.0510.0510.0000.0000.0000.000
26B51LYS10.9790.96828.626-8.568-8.5680.0000.0000.0000.000
27B52LYS10.9600.97528.271-9.888-9.8880.0000.0000.0000.000
28B53GLY00.0570.03024.6340.3480.3480.0000.0000.0000.000
29B54GLN0-0.076-0.04324.2640.3030.3030.0000.0000.0000.000
30B55THR0-0.0060.00625.688-0.006-0.0060.0000.0000.0000.000
31B56LYS10.8280.90217.939-15.680-15.6800.0000.0000.0000.000
32B57LYS10.9360.97020.866-12.268-12.2680.0000.0000.0000.000
33B58GLU-1-0.819-0.88621.82811.13611.1360.0000.0000.0000.000
34B59ILE00.0110.00521.415-0.024-0.0240.0000.0000.0000.000
35B60GLU-1-0.774-0.83717.03316.28316.2830.0000.0000.0000.000
36B61LYS10.8920.93318.864-11.469-11.4690.0000.0000.0000.000
37B62ARG10.8130.88820.710-10.694-10.6940.0000.0000.0000.000
38B63THR0-0.015-0.01019.4520.0200.0200.0000.0000.0000.000
39B64LYS10.8320.90715.625-14.874-14.8740.0000.0000.0000.000
40B65THR0-0.0140.01314.6281.1551.1550.0000.0000.0000.000
41B66LYS10.8870.95010.214-25.103-25.1030.0000.0000.0000.000
42B67ILE0-0.018-0.01614.4460.1430.1430.0000.0000.0000.000
43B68THR0-0.006-0.00914.8660.2750.2750.0000.0000.0000.000
44B69ILE0-0.018-0.01917.310-0.316-0.3160.0000.0000.0000.000
45B70ASP-1-0.787-0.87120.69613.77713.7770.0000.0000.0000.000
46B71SER0-0.071-0.06822.360-0.369-0.3690.0000.0000.0000.000
47B72GLU-1-0.941-0.94525.58510.31310.3130.0000.0000.0000.000
48B73THR0-0.069-0.06323.972-0.468-0.4680.0000.0000.0000.000
49B74GLY00.0170.00025.834-0.323-0.3230.0000.0000.0000.000
50B75GLU-1-0.812-0.84521.09213.84413.8440.0000.0000.0000.000
51B76VAL0-0.026-0.02520.0650.0570.0570.0000.0000.0000.000
52B77TRP00.0600.03114.889-0.312-0.3120.0000.0000.0000.000
53B78ILE0-0.063-0.03516.204-0.204-0.2040.0000.0000.0000.000
54B79THR00.0400.01410.7570.3570.3570.0000.0000.0000.000
55B80SER00.0510.02910.039-1.338-1.3380.0000.0000.0000.000
56B81THR0-0.059-0.0389.3581.3711.3710.0000.0000.0000.000
57B82LYS10.9120.9307.973-21.029-21.0290.0000.0000.0000.000
58B83GLU-1-0.800-0.8829.89818.07218.0720.0000.0000.0000.000
59B84THR0-0.062-0.04112.885-0.996-0.9960.0000.0000.0000.000
60B85GLU-1-0.867-0.90514.81814.25714.2570.0000.0000.0000.000
61B86ASP-1-0.793-0.88417.83012.62012.6200.0000.0000.0000.000
62B87PRO00.028-0.00517.6890.5640.5640.0000.0000.0000.000
63B88LEU00.0220.00718.5450.4370.4370.0000.0000.0000.000
64B89ALA0-0.021-0.00117.807-0.244-0.2440.0000.0000.0000.000
65B90VAL00.0300.00714.633-0.386-0.3860.0000.0000.0000.000
66B91TRP0-0.013-0.00716.624-0.483-0.4830.0000.0000.0000.000
67B92LYS10.8910.94821.107-12.346-12.3460.0000.0000.0000.000
68B93ALA0-0.008-0.00319.588-0.505-0.5050.0000.0000.0000.000
69B94ARG10.7900.87920.204-13.666-13.6660.0000.0000.0000.000
70B95ASP-1-0.776-0.88021.97911.56811.5680.0000.0000.0000.000
71B96ILE0-0.021-0.01824.398-0.568-0.5680.0000.0000.0000.000
72B97VAL0-0.007-0.00621.838-0.471-0.4710.0000.0000.0000.000
73B98LEU00.0090.01225.213-0.482-0.4820.0000.0000.0000.000
74B99ALA0-0.005-0.00727.464-0.472-0.4720.0000.0000.0000.000
75B100ILE0-0.035-0.01527.038-0.425-0.4250.0000.0000.0000.000
76B101GLY00.0460.02428.944-0.299-0.2990.0000.0000.0000.000
77B102ARG10.8250.89830.006-9.619-9.6190.0000.0000.0000.000
78B103GLY00.0200.02033.212-0.339-0.3390.0000.0000.0000.000
79B104PHE0-0.027-0.01232.994-0.238-0.2380.0000.0000.0000.000
80B105SER00.0240.00533.3160.2070.2070.0000.0000.0000.000
81B106PRO00.0610.00228.994-0.010-0.0100.0000.0000.0000.000
82B107GLU-1-0.954-0.96330.7148.4678.4670.0000.0000.0000.000
83B108ARG10.8590.90233.096-8.037-8.0370.0000.0000.0000.000
84B109ALA0-0.0080.00229.567-0.018-0.0180.0000.0000.0000.000
85B110PHE00.020-0.01025.3510.1820.1820.0000.0000.0000.000
86B111ARG10.7570.86929.762-8.261-8.2610.0000.0000.0000.000
87B112LEU0-0.022-0.00727.871-0.063-0.0630.0000.0000.0000.000
88B113LEU0-0.029-0.00824.7260.3550.3550.0000.0000.0000.000
89B114ASN0-0.067-0.03627.6080.2620.2620.0000.0000.0000.000
90B115GLU-1-0.861-0.92728.76010.45010.4500.0000.0000.0000.000
91B116GLY0-0.030-0.00830.678-0.343-0.3430.0000.0000.0000.000
92B117GLU-1-0.877-0.93731.5548.3178.3170.0000.0000.0000.000
93B118TYR00.0300.00729.1810.2060.2060.0000.0000.0000.000
94B119LEU0-0.012-0.01628.531-0.329-0.3290.0000.0000.0000.000
95B120GLU-1-0.787-0.88031.6838.8488.8480.0000.0000.0000.000
96B121ILE0-0.039-0.03830.209-0.124-0.1240.0000.0000.0000.000
97B122ILE00.0100.02234.608-0.039-0.0390.0000.0000.0000.000
98B123ASN00.002-0.01635.7160.0430.0430.0000.0000.0000.000
99B124LEU0-0.034-0.02938.716-0.202-0.2020.0000.0000.0000.000
100B125THR0-0.061-0.07240.451-0.154-0.1540.0000.0000.0000.000
101B126ASP-1-0.811-0.86638.7388.0008.0000.0000.0000.0000.000
102B127ILE0-0.036-0.00742.350-0.094-0.0940.0000.0000.0000.000
103B128ILE0-0.076-0.03945.322-0.151-0.1510.0000.0000.0000.000
104B129ILE00.0540.02946.683-0.141-0.1410.0000.0000.0000.000
105B130GLY0-0.009-0.00448.713-0.078-0.0780.0000.0000.0000.000
106B131ASN00.0060.00850.224-0.167-0.1670.0000.0000.0000.000
107B132GLU-1-0.747-0.84652.7885.5515.5510.0000.0000.0000.000
108B133LYS10.8950.94452.387-5.390-5.3900.0000.0000.0000.000
109B134ASN00.019-0.01450.4930.0300.0300.0000.0000.0000.000
110B135ALA00.0180.01650.1710.0110.0110.0000.0000.0000.000
111B136LEU00.0750.04542.7550.0100.0100.0000.0000.0000.000
112B137PRO0-0.035-0.02946.9960.0370.0370.0000.0000.0000.000
113B138ARG10.8770.93148.270-5.853-5.8530.0000.0000.0000.000
114B139VAL00.0280.01946.432-0.062-0.0620.0000.0000.0000.000
115B140ARG10.9390.96442.860-7.195-7.1950.0000.0000.0000.000
116B141GLY00.0100.00846.5650.0030.0030.0000.0000.0000.000
117B142ARG10.7740.87749.838-6.110-6.1100.0000.0000.0000.000
118B143ILE00.0520.03444.469-0.068-0.0680.0000.0000.0000.000
119B144ILE00.0030.00844.7020.0170.0170.0000.0000.0000.000
120B145GLY00.0320.01947.621-0.065-0.0650.0000.0000.0000.000
121B146ARG10.9630.96251.123-5.562-5.5620.0000.0000.0000.000
122B147LYS10.9680.97051.570-5.679-5.6790.0000.0000.0000.000
123B148GLY00.0510.03948.4060.0510.0510.0000.0000.0000.000
124B149ARG10.9080.95548.695-5.759-5.7590.0000.0000.0000.000
125B150THR00.0270.01449.257-0.069-0.0690.0000.0000.0000.000
126B151ARG10.8790.93442.399-7.149-7.1490.0000.0000.0000.000
127B152GLN00.0550.04046.040-0.046-0.0460.0000.0000.0000.000
128B153ILE0-0.024-0.00647.6450.0180.0180.0000.0000.0000.000
129B154ILE00.0230.00544.3850.0040.0040.0000.0000.0000.000
130B155GLU-1-0.751-0.81841.6797.5047.5040.0000.0000.0000.000
131B156GLU-1-0.860-0.93344.7146.4066.4060.0000.0000.0000.000
132B157MET0-0.049-0.00947.501-0.039-0.0390.0000.0000.0000.000
133B158SER0-0.026-0.01843.6470.0430.0430.0000.0000.0000.000
134B159GLY00.0280.01443.0740.0790.0790.0000.0000.0000.000
135B160ALA00.0160.02739.6280.2020.2020.0000.0000.0000.000
136B161SER0-0.070-0.03437.299-0.091-0.0910.0000.0000.0000.000
137B162VAL00.003-0.00838.1530.1540.1540.0000.0000.0000.000
138B163SER0-0.052-0.02136.698-0.153-0.1530.0000.0000.0000.000
139B164VAL0-0.021-0.01038.4130.0880.0880.0000.0000.0000.000
140B165TYR0-0.043-0.05234.090-0.109-0.1090.0000.0000.0000.000
141B166GLY00.0480.03038.1240.1470.1470.0000.0000.0000.000
142B167LYS10.9400.96037.444-8.510-8.5100.0000.0000.0000.000
143B168THR00.0510.04635.1780.0560.0560.0000.0000.0000.000
144B169VAL0-0.059-0.03738.457-0.145-0.1450.0000.0000.0000.000
145B170ALA00.0220.03234.2190.0600.0600.0000.0000.0000.000
146B171ILE0-0.050-0.04035.585-0.287-0.2870.0000.0000.0000.000
147B172ILE00.0440.01932.0460.2490.2490.0000.0000.0000.000
148B173GLY00.0510.02434.762-0.316-0.3160.0000.0000.0000.000
149B174ASN00.0910.06335.0810.1460.1460.0000.0000.0000.000
150B175PRO00.0510.00335.300-0.191-0.1910.0000.0000.0000.000
151B176ILE00.0160.01637.754-0.146-0.1460.0000.0000.0000.000
152B177GLN00.0110.01039.2270.0100.0100.0000.0000.0000.000
153B178ILE00.0140.00635.009-0.159-0.1590.0000.0000.0000.000
154B179GLU-1-0.730-0.82639.5226.7566.7560.0000.0000.0000.000
155B180ILE0-0.0060.01142.377-0.116-0.1160.0000.0000.0000.000
156B181ALA00.003-0.01041.575-0.141-0.1410.0000.0000.0000.000
157B182LYS10.8700.93838.262-8.176-8.1760.0000.0000.0000.000
158B183THR0-0.002-0.02242.635-0.100-0.1000.0000.0000.0000.000
159B184ALA0-0.034-0.01746.070-0.177-0.1770.0000.0000.0000.000
160B185ILE0-0.003-0.01241.830-0.135-0.1350.0000.0000.0000.000
161B186GLU-1-0.878-0.95042.7487.2087.2080.0000.0000.0000.000
162B187LYS10.8790.96046.383-6.343-6.3430.0000.0000.0000.000
163B188LEU0-0.027-0.00648.479-0.146-0.1460.0000.0000.0000.000
164B189ALA00.010-0.00446.400-0.110-0.1100.0000.0000.0000.000
165B190ARG10.9390.97448.195-6.434-6.4340.0000.0000.0000.000
166B191GLY00.0130.01850.999-0.114-0.1140.0000.0000.0000.000
167B192SER0-0.015-0.00752.900-0.138-0.1380.0000.0000.0000.000
168B193PRO00.0180.02354.8020.0670.0670.0000.0000.0000.000
169B194HIS00.0340.00652.175-0.100-0.1000.0000.0000.0000.000
170B195GLY00.0220.01855.4880.0410.0410.0000.0000.0000.000
171B196SER0-0.079-0.05556.516-0.002-0.0020.0000.0000.0000.000
172B197VAL00.0130.00850.5950.0380.0380.0000.0000.0000.000
173B198TYR0-0.025-0.03152.2720.0370.0370.0000.0000.0000.000
174B199ARG11.0411.01954.448-5.242-5.2420.0000.0000.0000.000
175B200TYR0-0.074-0.04947.864-0.104-0.1040.0000.0000.0000.000
176B201LEU00.0300.01348.4110.0550.0550.0000.0000.0000.000
177B202GLU-1-0.885-0.95451.7065.7515.7510.0000.0000.0000.000
178B203ARG10.7690.85753.415-5.828-5.8280.0000.0000.0000.000
179B204ARG10.8010.87446.396-6.583-6.5830.0000.0000.0000.000
180B205LYS10.8480.91249.473-6.210-6.2100.0000.0000.0000.000
181B206LYS10.9340.96951.276-5.347-5.3470.0000.0000.0000.000
182B207ASP-1-0.826-0.85350.8895.9435.9430.0000.0000.0000.000
183B208LEU0-0.0010.00047.5950.1050.1050.0000.0000.0000.000